[2023-06-16 19:18:16,560] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:18:16,562] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:18:16,562] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f6f8637-2999-422d-bfd5-2097b38b5791/dqc_reference
[2023-06-16 19:18:17,647] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:18:17,648] [INFO] Task started: Prodigal
[2023-06-16 19:18:17,648] [INFO] Running command: gunzip -c /var/lib/cwl/stgbaec6c9c-0575-452c-aae7-3f62e3571f5c/GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna.gz | prodigal -d GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/cds.fna -a GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:18:20,738] [INFO] Task succeeded: Prodigal
[2023-06-16 19:18:20,738] [INFO] Task started: HMMsearch
[2023-06-16 19:18:20,738] [INFO] Running command: hmmsearch --tblout GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f6f8637-2999-422d-bfd5-2097b38b5791/dqc_reference/reference_markers.hmm GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:18:20,925] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:18:20,926] [INFO] Found 6/6 markers.
[2023-06-16 19:18:20,945] [INFO] Query marker FASTA was written to GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/markers.fasta
[2023-06-16 19:18:20,946] [INFO] Task started: Blastn
[2023-06-16 19:18:20,946] [INFO] Running command: blastn -query GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f6f8637-2999-422d-bfd5-2097b38b5791/dqc_reference/reference_markers.fasta -out GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:18:21,506] [INFO] Task succeeded: Blastn
[2023-06-16 19:18:21,510] [INFO] Selected 19 target genomes.
[2023-06-16 19:18:21,510] [INFO] Target genome list was writen to GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/target_genomes.txt
[2023-06-16 19:18:21,513] [INFO] Task started: fastANI
[2023-06-16 19:18:21,513] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaec6c9c-0575-452c-aae7-3f62e3571f5c/GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna.gz --refList GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/target_genomes.txt --output GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:18:29,887] [INFO] Task succeeded: fastANI
[2023-06-16 19:18:29,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f6f8637-2999-422d-bfd5-2097b38b5791/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:18:29,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f6f8637-2999-422d-bfd5-2097b38b5791/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:18:29,889] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:18:29,889] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 19:18:29,889] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-16 19:18:29,891] [INFO] DFAST Taxonomy check result was written to GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/tc_result.tsv
[2023-06-16 19:18:29,891] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:18:29,891] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:18:29,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f6f8637-2999-422d-bfd5-2097b38b5791/dqc_reference/checkm_data
[2023-06-16 19:18:29,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:18:29,918] [INFO] Task started: CheckM
[2023-06-16 19:18:29,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/checkm_input GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/checkm_result
[2023-06-16 19:18:45,544] [INFO] Task succeeded: CheckM
[2023-06-16 19:18:45,545] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:18:45,561] [INFO] ===== Completeness check finished =====
[2023-06-16 19:18:45,561] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:18:45,562] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/markers.fasta)
[2023-06-16 19:18:45,562] [INFO] Task started: Blastn
[2023-06-16 19:18:45,562] [INFO] Running command: blastn -query GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f6f8637-2999-422d-bfd5-2097b38b5791/dqc_reference/reference_markers_gtdb.fasta -out GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:18:46,542] [INFO] Task succeeded: Blastn
[2023-06-16 19:18:46,545] [INFO] Selected 13 target genomes.
[2023-06-16 19:18:46,545] [INFO] Target genome list was writen to GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:18:46,550] [INFO] Task started: fastANI
[2023-06-16 19:18:46,550] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaec6c9c-0575-452c-aae7-3f62e3571f5c/GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna.gz --refList GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/target_genomes_gtdb.txt --output GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:18:52,117] [INFO] Task succeeded: fastANI
[2023-06-16 19:18:52,122] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:18:52,123] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_905201505.1	s__Gallispira sp905201505	100.0	612	624	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__Gallispira	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900551755.1	s__Gallispira sp900551755	80.0775	213	624	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__Gallispira	95.0	99.95	99.95	0.89	0.89	2	-
GCF_904395805.1	s__Gallispira edinburgensis	79.9334	333	624	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__Gallispira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543365.1	s__Gallispira sp900543365	79.7708	236	624	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__Gallispira	95.0	99.75	99.35	0.91	0.83	4	-
GCA_900760465.1	s__HGM11788 sp900760465	77.799	141	624	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__HGM11788	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545305.1	s__CAG-274 sp900545305	77.4714	114	624	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__CAG-274	95.0	98.57	98.54	0.89	0.87	5	-
GCA_000432155.1	s__CAG-274 sp000432155	77.3712	118	624	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__CAG-274	95.0	98.95	98.88	0.91	0.89	4	-
--------------------------------------------------------------------------------
[2023-06-16 19:18:52,124] [INFO] GTDB search result was written to GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/result_gtdb.tsv
[2023-06-16 19:18:52,125] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:18:52,127] [INFO] DFAST_QC result json was written to GCA_905201505.1_ERR321572-mag-bin.22_genomic.fna/dqc_result.json
[2023-06-16 19:18:52,127] [INFO] DFAST_QC completed!
[2023-06-16 19:18:52,127] [INFO] Total running time: 0h0m36s